Train
Recently, train routes have another and even more valuable connection to cycling. In many cases, local train routes that have been eliminated due to depopulation have been turned into bikepaths. This invariably creates the perfect bikepath: level, scenic and linking two relatively significant rural destinations.
In Japan, English train schedules are few and far between. No matter. You may not read Japanese, but trust me: you'll be able to figure out the Japanese train schedule (or jikokuhyo), which can be purchased at any major bookstore. I was using them after only six months in the country, planning trips on little commuter ferries or overnight trains with complicated connections. Use an English map to determine where you want to start and end up, then find the same places on the train and ferry route maps in the front of the book. It's surprisingly easy. Just to be sure, check your plans with someone at the train station before you leave (the travel offices in major stations are happy to do this for you).
Using the Japanese train schedule also ensures that you'll be able to find your way home from little podunk stations way out in the boonies. I can guarantee that you won't find an English guide in such places. By the way, "train schedule" is a misnomer: this book, updated monthly, actually contains information on virtually all transit throughout the country: planes, trains, buses, special tours, you name it. Great for browsing.
If you don't want to spend the 800 yen or so for the guide, you should know that travel agencies in Japan - and even some Japanese travel agencies and airline offices and so on located in other countries - often have older copies of the Japanese train schedule that they no longer need, and they'll often give them to you free of charge. These are useful at the planning stage, but naturally you should confirm your connections using a current schedule.
If you're unable to find a train schedule, don't worry: one of the ex-national railway companies (JR West) now offers an Internet site (in Japanese) called "JR Odekake-Net" ("odekake" meaning "outing") that provides time and connection information for traveling between any two train stations in Japan:
In the near future, this site will provide more details on how to use this very cool (but still a bit problemataic) new tool.
The major types of trains that run in Japan are listed below in order of increasing speed (and price):
Futsuu (local) trains are OK for short hops.
Kaisoku trains are commuter expresses that make fewer stops but do not require an express ticket. Often they run at peak commuting times only. Commuter expresses of this type are often called Tsukin-Kaisoku. Special mention should be made of the JR shinkaisoku trains that run in urban areas (Kansai, Nagoya, Yokohama-Tokyo); these are express trains that do not require an express ticket, allowing you to get places rapidly at regular fare. Normally they make multiple stops at both ends of the run and speed through the middle with very few stops.
Kyuko are the standard express trains, but there seem to be fewer and fewer of them around compared to the ubiquitous tokkyu. If you have a choice of an overnight tokkyu or kyuko, by all means choose the kyuko - you'll save quite a bit of money if it's any distance at all.
Tokkyu are the so-called "limited express" trains, "limited" meaning fewer stops. The charges can be quite high, and some make as many stops as a kyuko would. Check the schedule and make your own judgment as to whether it's worth the extra fare. For many destinations, a tokkyu will be your only option. Some tokkyu have sleeper cars as well; however, this automatically adds around 6800 yen to the price of the ticket, which is what you'd pay for a good night's sleep in a business hotel. In my experience, this is something you're not likely to get on a train. If you've somehow managed to fall asleep, a crew will come by in the early morning to roust you out of bed so they can convert the berths back into seats. It’s worth trying once for the experience.
Shinkansen are the famous bullet trains. They are horrendously expensive - in fact, the shinkansen express ticket almost doubles the price of the fare. Accordingly, unless there's no other practical way to get to your destination (and often there isn’t), I try to avoid these. Note that the proliferation of local airports and more reasonable airline bike handling policies have made flying a better option in many cases.
For other reference materials that you may find useful in route planning, see RESOURCES.